Bear with me, this one is a bit convoluted.

Problem - crushed gold ore signal sets depleted acid recipe in filtration plant. It should set "filter dirty water [gold ore icon]" .

I am feeding the resources stockpiled, divided by some constants, and more processing which isn't relevant, into the filtration plants to tell them which recipe they should use for reclaiming dirty water. This disposes of the large volume of waste while sending it to whatever is most lacking.

But 'need gold'->crushed gold signal is setting the 'wrong' recipe. This shuts down most of the plants as they are unable to take dirty water, leading to a plethora of problems in my base and additionally an even greater gold shortfall. Gold ore sets no signal. I don't know how the internal game logic decides how to set recipes based on ENTITY signals, but if it is at all possible, this should be overridden. I can't conceive of a good case for this recipe needing to be able to be set by signal - only very bad cases like sushi fluid systems.

Even "silver concentrate" sets an appropriate recipe, albeit one which doesn't have silver in the name.

Alternatively, does anyone have a functional workaround for this? (setting crushed stone, the primary output from the desired recipe, doesn't set the desired recipe)

Hmm, this is an odd one. Sending crushed copper will set the gold filtration recipe for you (so there's your workaround), it's not AFAICT possible to select the copper one with circuits at all, and crushed gold signal will be different depending on whether BrimStuff's waste processing is turned on or not. (Though turning that off also keeps the game from loading with the current version of ATOM, oops.)

Seems pretty obvious to me that crushed copper should select the recipe that only produces copper, and acid treatment should have it's own signal (since I prefer not to remove existing functionality, even if I also don't see much need for it), but I'm not entirely sure how to make that happen. At any rate, it's on my list of things to dig into further now.